Many theories exist to predict the growth of Microcystis, one major type of toxic cyanobacteria that form harmful algal blooms. However, the impacts of suspended particles, which are ubiquitous in freshwater, on Microcystis growth have not been fully understood. Here, we show that a smectite clay can inhibit the growth of Microcystis aeruginosa, a typical toxic freshwater cyanobacterium, through physical clay-cell interactions. We grow M. aeruginosa under identical growth conditions in three nutrient solutions: one pure solution, one with a synthetic and transparent clay, and another one chemically modified by clay but with clay particles removed. Cells in pure solution and chemically-modified solution grow equally well, while cells in solutions with the physical presence of clay do not grow nor produce pigments. Microscopic imaging of clay-cell interactions suggests that the inhibition of the growth of M. aeruginosa by clay is due to the physical encapsulation of cells in clay.